This study investigates the bacterial community composition along a 2000 km salinity gradient in the Baltic Sea, one of the world's largest brackish water environments. Using 454 pyrosequencing of partial 16S rRNA genes, the researchers identified a diverse combination of freshwater and marine bacterial groups, as well as unique populations adapted to brackish conditions. The bacterial community composition changed significantly at both broad and finer phylogenetic levels within the salinity gradient. Unlike multicellular organisms, which show a decline in diversity in brackish waters, no significant reduction in bacterial diversity was observed. The study suggests that the rapid adaptation rate of bacteria has enabled various lineages to fill ecological niches that are challenging for higher organisms. The results provide a detailed description of an autochthonous brackish microbiome and highlight the importance of salinity in structuring bacterial communities.This study investigates the bacterial community composition along a 2000 km salinity gradient in the Baltic Sea, one of the world's largest brackish water environments. Using 454 pyrosequencing of partial 16S rRNA genes, the researchers identified a diverse combination of freshwater and marine bacterial groups, as well as unique populations adapted to brackish conditions. The bacterial community composition changed significantly at both broad and finer phylogenetic levels within the salinity gradient. Unlike multicellular organisms, which show a decline in diversity in brackish waters, no significant reduction in bacterial diversity was observed. The study suggests that the rapid adaptation rate of bacteria has enabled various lineages to fill ecological niches that are challenging for higher organisms. The results provide a detailed description of an autochthonous brackish microbiome and highlight the importance of salinity in structuring bacterial communities.